The Role of RNA Secondary Structure in Viral Assembly

Abstract

Some small icosahedral RNA viruses (e.g., MS2) require a specific packaging signal for the formation of virus particles. Others (e.g., cowpea chlorotic mottle virus (CCMV); Pariacoto virus (PaV)) are able to encapsidate a wide variety of RNAs, forming virus-like particles (VLPs) whose structure are only slightly different from that of the wild-type virus. We have determined the structure of the genomic RNA of satellite tobacco mosaic virus (STMV) in an in vitro transcript (see image below). This structure is very different from the structure of STMV RNA probed inside the virus by Schroeder et al. (BJ 101:167 (2011)), which consists of a string of stem-loops connected by single-stranded regions. We have also developed all-atom models for three viruses: PaV (using a hypothetical secondary structure and a non-viral sequence); STMV (using the true sequence and the Schroeder secondary structure); and MS2 (using the true sequence and a hypothetical secondary structure). In this talk, we discuss the implications of these secondary structures and three-dimensional models for the pathways of viral assembly.